Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads
view test-data/input/SRR17907745_kraken_style_bracken_report.txt @ 3:899a650587ed draft default tip
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 24535690aedb81353cf5e036dc4577022d9604ad
| author | public-health-bioinformatics |
|---|---|
| date | Thu, 27 Oct 2022 19:13:25 +0000 |
| parents | |
| children |
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100.00 2371444 0 R 1 root 100.00 2371444 0 R1 131567 cellular organisms 99.99 2371306 0 D 2 Bacteria 99.99 2371287 0 P 1224 Proteobacteria 99.99 2371241 0 C 1236 Gammaproteobacteria 99.99 2371241 0 O 91347 Enterobacterales 99.25 2353760 0 F 543 Enterobacteriaceae 53.04 1257733 0 G 570 Klebsiella 44.15 1046984 1046984 S 1463165 Klebsiella quasipneumoniae 7.73 183381 183381 S 573 Klebsiella pneumoniae 0.26 6092 0 G1 2608929 unclassified Klebsiella 0.19 4605 4605 S 2015795 Klebsiella sp. LY 0.03 757 757 S 2267618 Klebsiella sp. P1CD1 0.01 318 318 S 2787706 Klebsiella sp. BDA134-6 0.02 410 410 S 2488567 Klebsiella sp. FDAARGOS_511 0.32 7585 7585 S 244366 Klebsiella variicola 0.08 1853 1853 S 571 Klebsiella oxytoca 0.05 1294 1294 S 548 Klebsiella aerogenes 0.05 1261 1261 S 2026240 Klebsiella quasivariicola 0.19 4517 4517 S 1134687 Klebsiella michiganensis 0.17 3937 3937 S 2058152 Klebsiella grimontii 0.03 659 659 S 2489010 Klebsiella africana 0.01 164 164 S 2153354 Klebsiella huaxiensis 33.69 798958 0 G 561 Escherichia 33.68 798809 798809 S 562 Escherichia coli 0.01 149 149 S 564 Escherichia fergusonii 6.10 144567 0 G 547 Enterobacter 6.09 144531 0 G1 354276 Enterobacter cloacae complex 3.68 87241 87241 S 158836 Enterobacter hormaechei 2.40 56903 56903 S 550 Enterobacter cloacae 0.01 282 282 S 1812935 Enterobacter roggenkampii 0.00 91 91 S 208224 Enterobacter kobei 0.00 13 13 S 61645 Enterobacter asburiae 0.00 35 0 G1 2608935 unclassified Enterobacter 0.00 18 18 S 2596949 Enterobacter sp. E76 0.00 17 17 S 2500132 Enterobacter sp. N18-03635 5.77 136773 0 G 544 Citrobacter 5.65 134026 0 G1 1344959 Citrobacter freundii complex 5.65 133878 133878 S 546 Citrobacter freundii 0.01 148 148 S 1639133 Citrobacter portucalensis 0.12 2728 0 G1 2644389 unclassified Citrobacter 0.10 2352 2352 S 2742632 Citrobacter sp. RHBSTW-00053 0.02 375 375 S 2742638 Citrobacter sp. RHBSTW-00137 0.00 19 19 S 67825 Citrobacter rodentium 0.58 13709 0 G 590 Salmonella 0.21 5059 0 G1 2614656 unclassified Salmonella 0.09 2074 2074 S 2500542 Salmonella sp. SSDFZ54 0.13 2985 2985 S 599 Salmonella sp. 0.36 8649 8649 S 28901 Salmonella enterica 0.03 746 0 G 620 Shigella 0.03 746 746 S 621 Shigella boydii 0.02 554 0 G 160674 Raoultella 0.02 431 431 S 54291 Raoultella ornithinolytica 0.00 89 89 S 577 Raoultella terrigena 0.00 33 33 S 575 Raoultella planticola 0.02 409 0 G 1330547 Kosakonia 0.02 387 387 S 283686 Kosakonia radicincitans 0.00 22 22 S 497725 Kosakonia oryzae 0.01 182 0 G 83654 Leclercia 0.01 182 0 G1 2627398 unclassified Leclercia 0.01 182 182 S 2815358 Leclercia sp. 4-9-1-25 0.00 46 0 G 1330546 Pluralibacter 0.00 35 35 S 1334193 [Enterobacter] lignolyticus 0.00 11 11 S 61647 Pluralibacter gergoviae 0.00 21 0 G 2815296 Jejubacter 0.00 21 21 S 2579935 Jejubacter calystegiae 0.00 13 0 G 158483 Cedecea 0.00 13 13 S 158822 Cedecea neteri 0.00 11 0 G 1330545 Lelliottia 0.00 11 11 S 61646 Lelliottia amnigena 0.00 11 0 G 2726810 Scandinavium 0.00 11 11 S 1851514 Scandinavium goeteborgense 0.00 11 0 G 1335483 Shimwellia 0.00 11 11 S 563 Shimwellia blattae 0.00 10 0 G 2055880 Pseudescherichia 0.00 10 10 S 566 Pseudescherichia vulneris 0.71 16876 0 F 1903409 Erwiniaceae 0.71 16788 0 G 82986 Tatumella 0.71 16788 0 G1 2649542 unclassified Tatumella 0.71 16788 16788 S 2487345 Tatumella sp. TA1 0.00 53 0 G 53335 Pantoea 0.00 33 33 S 553 Pantoea ananatis 0.00 19 19 S 66269 Pantoea stewartii 0.00 34 0 G 551 Erwinia 0.00 34 34 S 79967 Erwinia pyrifoliae 0.02 525 0 F 1903411 Yersiniaceae 0.01 341 0 G 629 Yersinia 0.01 190 0 G1 1649845 Yersinia pseudotuberculosis complex 0.01 190 190 S 633 Yersinia pseudotuberculosis 0.01 151 151 S 28152 Yersinia kristensenii 0.01 151 0 G 34037 Rahnella 0.00 79 79 S 34038 Rahnella aquatilis 0.00 71 0 G1 2635087 unclassified Rahnella 0.00 71 71 S 657334 Rahnella sp. WMR42 0.00 31 0 G 613 Serratia 0.00 31 31 S 615 Serratia marcescens 0.00 79 0 F 1903410 Pectobacteriaceae 0.00 61 0 G 122277 Pectobacterium 0.00 61 61 S 2488639 Pectobacterium versatile 0.00 18 0 G 71655 Brenneria 0.00 18 18 S 1109412 Brenneria goodwinii 0.00 46 0 C 28211 Alphaproteobacteria 0.00 46 0 O 356 Hyphomicrobiales 0.00 46 0 F 41294 Bradyrhizobiaceae 0.00 46 0 G 1073 Rhodopseudomonas 0.00 46 46 S 1076 Rhodopseudomonas palustris 0.00 19 0 D1 1783272 Terrabacteria group 0.00 19 0 P 1239 Firmicutes 0.00 19 0 C 91061 Bacilli 0.00 19 0 O 1385 Bacillales 0.00 19 0 F 90964 Staphylococcaceae 0.00 19 0 G 1279 Staphylococcus 0.00 19 19 S 1280 Staphylococcus aureus 0.01 138 0 D 2759 Eukaryota 0.01 138 0 D1 33154 Opisthokonta 0.01 138 0 K 33208 Metazoa 0.01 138 0 K1 6072 Eumetazoa 0.01 138 0 K2 33213 Bilateria 0.01 138 0 K3 33511 Deuterostomia 0.01 138 0 P 7711 Chordata 0.01 138 0 P1 89593 Craniata 0.01 138 0 P2 7742 Vertebrata 0.01 138 0 P3 7776 Gnathostomata 0.01 138 0 P4 117570 Teleostomi 0.01 138 0 P5 117571 Euteleostomi 0.01 138 0 P6 8287 Sarcopterygii 0.01 138 0 C 1338369 Dipnotetrapodomorpha 0.01 138 0 C1 32523 Tetrapoda 0.01 138 0 C2 32524 Amniota 0.01 138 0 C 40674 Mammalia 0.01 138 0 C1 32525 Theria 0.01 138 0 C2 9347 Eutheria 0.01 138 0 C3 1437010 Boreoeutheria 0.01 138 0 C4 314146 Euarchontoglires 0.01 138 0 O 9443 Primates 0.01 138 0 O1 376913 Haplorrhini 0.01 138 0 O2 314293 Simiiformes 0.01 138 0 O3 9526 Catarrhini 0.01 138 0 O4 314295 Hominoidea 0.01 138 0 F 9604 Hominidae 0.01 138 0 F1 207598 Homininae 0.01 138 0 G 9605 Homo 0.01 138 138 S 9606 Homo sapiens